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In 3135, Thaddeus had just arrived from New Aragon, failing to prevent the Capellan Confederation from taking that world. Thaddeus had been secretly planning and setting ground work for alliances within the Republic to create neighborhoods of worlds which would act as "pocket fortresses" to keep larger interstellar nations from swallowing them up easily. He revealed his plan to Exarch Levin in a private meeting on September 11th, after "Fortress Republic" was revealed. His plan involved neighborhoods in Prefectures VI, VII, & VIII, all adjacent to Marik space and areas he knew, and it called for him to be outside of the fortress to accomplish it. To avoid suspicion of his ambitions, Thaddeus offered to give his plans which he had been working on for months to Levin to hand to another person to handle. Levin allowed Thaddeus to proceed with his plans and arranged for similar neighborhoods to be established in other prefectures.

By December 3135, Thaddeus led a multi-world force under the flag of the Shiloh Alliance on their first campaign to invade and conqueror the world of Phecda. This campaign failed because upon arrival his unit was forced to withdraw after encountering the newly formed mercenary unit, The Wolf Hunters.

Thaddeus then secretly arranged for the Wolf Hunters to attack New Canton on a raid. The mercenary unit was initially successful, but surprised when the remains of the Steel Wolves faction lead by Galaxy Commander Varnoff Fetladral arrived in October 3136 to kill Anastasia Kerensky, leader of the Wolf Hunters. Feeling that New Canton was too valuable to be damaged Thaddeus ordered the Wolf Hunters to engage the Steel Wolves to prevent what he thought was a full-raid on the planet. Instead Anastasia challenged Varnoff Fetladral to a Trial of Grievance to stop the attack and limit the combatants to the two of them and to end the Steel Wolves hounding of the Wolf Hunters. Anastasia was victorious and there was no further conflict between the two forces.

Because there was no battle for the planet and no threat of raid from this conflict Thaddeus failed to convince the government of New Canton of the value of joining his Tall Trees Union.

In March of 3137, Thaddeus was elected to the rank of Warden of the Covenant Worlds, a small organization of planets which came together for self-defense. The world leaders of the Covenant felt that Thaddeus was the best person to lead their military forces in these trying times. Later that year Thaddeus had determined that Covenant Worlds needed a more powerful partner-nation if it was to have a chance to survive and so he traveled to see Jessica Halas-Hughes Marik, Captain-General of the Oriente Protectorate and her husband Sir Philip Hughes. After getting to know one another, Jessica revealed to Thaddeus that she knew that he was setting up small pocket nations in the former prefectures of the Republic. She had seen signs of the efforts he had taken to begin the process of unification within the League worlds. Thaddeus admitted this to be true and revealed his insight that the Republic was rotting from the inside out. He had known this since he became a Paladin and felt that reforming the League would be the only way to give people the best chance of surviving the coming age.

Phillip approached Thaddeus and asked him to marry his wife, purely as a political union of convenience. This marriage would allow Jessica and Thaddeus to adopt their children, thereby making them true Mariks and so able to become new leaders in a reborn Free Worlds League with a legal claim to the hallowed Marik name. Thaddeus was surprised by this request but, after thinking through the implications, ultimately agreed to the political marriage.

Thaddeus and his Covenant Worlds Expedition was then called upon to help fight the Lyran invasion of Free Worlds League space. Later that year his force attacked a Lyran garrison on Savannah and recaptured the world in the name of the League.

After Oriente sent its elite combat battalion Eagle’s Talons into Kwamashu in February of 3138, the Oriente forces were blamed for that world's ecological collapse, triggering war between the Duchy of Andurien and the Oriente Protectorate. In response Thaddeus led the 1st Covenant World Expedition against the 4th Andurien Cavalry‎ on El Giza in early June.

On July 15th, Thaddeus led his forces in a brutal battle for the planet against 2nd Andurien Guard and the Mosiro Planetary Militia (MPM) in commercial center of the city of Al-Hassam.[4] The Andurien force fought from building to building, effectively destroying most of the city's commercial areas while the MPM fought in underground traffic tunnels beneath the city.

Convenant intelligence agents discovered evidence that raised doubts about who caused the "Kwamashu Incident". Thaddeus ceased the military campaign and took the evidence to the Captain-General on Oriente, who was convinced that the conflict was pointless and should be stopped.

In August of 3138, Thaddeus and Philip Hughes enlisted Thaddeus' older brother Frederick Marik to assist in the creation of a new Free Worlds League. After the announcement of his marriage to Jessica there was a public outcry against Jessica "leaving" her husband, stirring up new factionalism against the League. In October Thaddeus married Jessica, thereby making her and all her children, whom he legally adopted, officially Mariks.

In April 3139, Thaddeus led the Homecoming expeditionary force consisting of all of the allied Protectorates, Duchies and other nations within former Free Worlds League space against the Regulan occupation of Atreus. On July 3rd, when the Free Worlds League was formally reestablished, Thaddeus was named its first Warden-General while his wife Jessica became the Captain General.

The new Warden-General would hold his position for less than three months. Thaddeus Marik led the defense of New Olympia against the advancing Clan Wolf, knowing that Alaric Wolf had to be killed in order to stall their advance. Hoping to defeat Wolf's force in detail, Thaddeus instead found himself out-thought by Alaric when his unit was caught in a vise between two Wolf forces. Alaric himself slew the Warden-General with direct hits on his cockpit.[3]